Critical assessment of DNA adenine methylation in eukaryotes using quantitative deconvolution

Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing

(2021) Alan Tourancheau et al.   NATURE METHODS

N6-methyladenine is incorporated into mammalian genome by DNA polymerase

(2020) Xiaoling Liu et al.   CELL RESEARCH

N6-Deoxyadenosine Methylation in Mammalian Mitochondrial DNA

(2020) Ziyang Hao et al.   MOLECULAR CELL

The origin of genomic N6-methyl-deoxyadenosine in mammalian cells

(2020) Michael U. Musheev et al.   Nature Chemical Biology

Protein phosphatase 2A promotes stomatal development by stabilizing SPEECHLESS in Arabidopsis

(2020) Chao Bian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

No evidence for DNA N6-methyladenine in mammals

(2020) Karolos Douvlataniotis et al.   Science Advances

Live yeast in juvenile diet induces species-specific effects on Drosophila adult behaviour and fitness

(2019) Juliette Murgier et al.   Scientific Reports

Sources of artifact in measurements of 6mA and 4mC abundance in eukaryotic genomic DNA

(2019) Zach K. O’Brown et al.   BMC GENOMICS

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

The bacterial epigenome

(2019) María A. Sánchez-Romero et al.   NATURE REVIEWS MICROBIOLOGY

Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis

(2019) Pedro H. Oliveira et al.   Nature Microbiology

Vertical Ultrafiltration-Facilitated DNA Digestion for Rapid and Sensitive UHPLC-MS/MS Detection of DNA Modifications

(2018) Weiyi Lai et al.   ANALYTICAL CHEMISTRY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

DNA N 6 -Adenine Methylation in Arabidopsis thaliana

(2018) Zhe Liang et al.   DEVELOPMENTAL CELL

Acetic Acid Bacteria in the Food Industry: Systematics, Characteristics and Applications

(2018) Rodrigo José Gomes et al.   FOOD TECHNOLOGY AND BIOTECHNOLOGY

Mapping and characterizing N6-methyladenine in eukaryotic genomes using single-molecule real-time sequencing

(2018) Shijia Zhu et al.   GENOME RESEARCH

N 6 -Methyladenine DNA Modification in the Human Genome

(2018) Chuan-Le Xiao et al.   MOLECULAR CELL

A reassessment of DNA-immunoprecipitation-based genomic profiling

(2018) Antonio Lentini et al.   NATURE METHODS

Active N6-Methyladenine Demethylation by DMAD Regulates Gene Expression by Coordinating with Polycomb Protein in Neurons

(2018) Bing Yao et al.   MOLECULAR CELL

N-methyladenine DNA Modification in Glioblastoma

(2018) Qi Xie et al.   CELL

Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate

(2018) Wilfried M. Guiblet et al.   GENOME RESEARCH

N6-methyldeoxyadenine is a transgenerational epigenetic signal for mitochondrial stress adaptation

(2018) Chengchuan Ma et al.   NATURE CELL BIOLOGY

Deciphering bacterial epigenomes using modern sequencing technologies

(2018) John Beaulaurier et al.   NATURE REVIEWS GENETICS

Single-nucleotide-resolution sequencing of human N6-methyldeoxyadenosine reveals strand-asymmetric clusters associated with SSBP1 on the mitochondrial genome

(2018) Casslynn W Q Koh et al.   NUCLEIC ACIDS RESEARCH

Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation

(2017) John Beaulaurier et al.   NATURE BIOTECHNOLOGY

Widespread adenine N6-methylation of active genes in fungi

(2017) Stephen J Mondo et al.   NATURE GENETICS

N6-adenine DNA methylation is associated with the linker DNA of H2A.Z-containing well-positioned nucleosomes in Pol II-transcribed genes in Tetrahymena

(2017) Yuanyuan Wang et al.   NUCLEIC ACIDS RESEARCH

DNA methylation on N6-adenine in mammalian embryonic stem cells

(2016) Tao P. Wu et al.   NATURE

Three decades of nanopore sequencing

(2016) David Deamer et al.   NATURE BIOTECHNOLOGY

MethSMRT: an integrative database for DNA N6-methyladenine and N4-methylcytosine generated by single-molecular real-time sequencing

(2016) Pohao Ye et al.   NUCLEIC ACIDS RESEARCH

Characterization of eukaryotic DNA N6-methyladenine by a highly sensitive restriction enzyme-assisted sequencing

(2016) Guan-Zheng Luo et al.   Nature Communications

The Epigenomic Landscape of Prokaryotes

(2016) Matthew J. Blow et al.   PLoS Genetics

Immune cell subsets and their gene expression profiles from human PBMC isolated by Vacutainer Cell Preparation Tube (CPT™) and standard density gradient

(2015) Christopher P. Corkum et al.   BMC IMMUNOLOGY

DNA Methylation on N6-Adenine in C. elegans

(2015) Eric Lieberman Greer et al.   CELL

N6-Methyladenine DNA Modification in Drosophila

(2015) Guoqiang Zhang et al.   CELL

N6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas

(2015) Ye Fu et al.   CELL

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12

(2015) Brian P. Anton et al.   PLoS One

Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes

(2015) John Beaulaurier et al.   Nature Communications

Evolutionally dynamic L1 regulation in embryonic stem cells

(2014) N. Castro-Diaz et al.   GENES & DEVELOPMENT

REBASE—a database for DNA restriction and modification: enzymes, genes and genomes

(2014) Richard J. Roberts et al.   NUCLEIC ACIDS RESEARCH

Improved nucleosome-positioning algorithm iNPS for accurate nucleosome positioning from sequencing data

(2014) Weizhong Chen et al.   Nature Communications

How Microbiomes Influence Metazoan Development:Insights from History andDrosophilaModeling of Gut-Microbe Interactions

(2013) Won-Jae Lee et al.   Annual Review of Cell and Developmental Biology

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases

(2012) E. E. Schadt et al.   GENOME RESEARCH

Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene

(2012) E. W. Loomis et al.   GENOME RESEARCH

Natural Transformation of an Engineered Helicobacter pylori Strain Deficient in Type II Restriction Endonucleases

(2012) X.-S. Zhang et al.   JOURNAL OF BACTERIOLOGY

Defining the core Arabidopsis thaliana root microbiome

(2012) Derek S. Lundberg et al.   NATURE

Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing

(2012) Gang Fang et al.   NATURE BIOTECHNOLOGY

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY